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Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction.

Mirvish ED, Shuda M.

Front Microbiol. 2016 May 13;7:676. doi: 10.3389/fmicb.2016.00676. Review.


Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.

Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S.

Viruses. 2016 Feb 19;8(2). pii: E53. doi: 10.3390/v8020053.


Merkel Cell Polyomavirus Small T Antigen Induces Cancer and Embryonic Merkel Cell Proliferation in a Transgenic Mouse Model.

Shuda M, Guastafierro A, Geng X, Shuda Y, Ostrowski SM, Lukianov S, Jenkins FJ, Honda K, Maricich SM, Moore PS, Chang Y.

PLoS One. 2015 Nov 6;10(11):e0142329. doi: 10.1371/journal.pone.0142329.


Preferential Amplification of Pathogenic Sequences.

Ge F, Parker J, Chul Choi S, Layer M, Ross K, Jilly B, Chen J.

Sci Rep. 2015 Jun 11;5:11047. doi: 10.1038/srep11047.


Interaction of human tumor viruses with host cell surface receptors and cell entry.

Schäfer G, Blumenthal MJ, Katz AA.

Viruses. 2015 May 22;7(5):2592-617. doi: 10.3390/v7052592. Review.


The CRISPR/Cas9 genome editing methodology as a weapon against human viruses.

White MK, Hu W, Khalili K.

Discov Med. 2015 Apr;19(105):255-62. Review.


Restricted protein phosphatase 2A targeting by Merkel cell polyomavirus small T antigen.

Kwun HJ, Shuda M, Camacho CJ, Gamper AM, Thant M, Chang Y, Moore PS.

J Virol. 2015 Apr;89(8):4191-200. doi: 10.1128/JVI.00157-15.


Black cat in a dark room: the absence of a directly oncogenic virus does not eliminate the role of an infectious agent in cutaneous T-cell lymphoma pathogenesis.

Dulmage BO, Feng H, Mirvish E, Geskin L.

Br J Dermatol. 2015;172(5):1449-51. doi: 10.1111/bjd.13519. No abstract available.


Viruses and human cancers: a long road of discovery of molecular paradigms.

White MK, Pagano JS, Khalili K.

Clin Microbiol Rev. 2014 Jul;27(3):463-81. doi: 10.1128/CMR.00124-13. Review.


RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

Xu G, Strong MJ, Lacey MR, Baribault C, Flemington EK, Taylor CM.

PLoS One. 2014 Feb 25;9(2):e89445. doi: 10.1371/journal.pone.0089445.


The conundrum of causality in tumor virology: the cases of KSHV and MCV.

Moore PS, Chang Y.

Semin Cancer Biol. 2014 Jun;26:4-12. doi: 10.1016/j.semcancer.2013.11.001. Review.


Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq.

Borozan I, Watt SN, Ferretti V.

PLoS One. 2013 Oct 30;8(10):e76935. doi: 10.1371/journal.pone.0076935.


Sensitive detection of viral transcripts in human tumor transcriptomes.

Schelhorn SE, Fischer M, Tolosi L, Altmüller J, Nürnberg P, Pfister H, Lengauer T, Berthold F.

PLoS Comput Biol. 2013;9(10):e1003228. doi: 10.1371/journal.pcbi.1003228.


Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.

DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA.

PLoS One. 2013 Sep 4;8(9):e73956. doi: 10.1371/journal.pone.0073956.


IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.

Dimon MT, Wood HM, Rabbitts PH, Arron ST.

PLoS One. 2013 May 23;8(5):e64546. doi: 10.1371/journal.pone.0064546.


Merkel cell polyomavirus: a newly discovered human virus with oncogenic potential.

Spurgeon ME, Lambert PF.

Virology. 2013 Jan 5;435(1):118-30. doi: 10.1016/j.virol.2012.09.029. Review.


CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes.

Borozan I, Wilson S, Blanchette P, Laflamme P, Watt SN, Krzyzanowski PM, Sircoulomb F, Rottapel R, Branton PE, Ferretti V.

BMC Bioinformatics. 2012 Aug 17;13:206. doi: 10.1186/1471-2105-13-206.


MCV and Merkel cell carcinoma: a molecular success story.

Arora R, Chang Y, Moore PS.

Curr Opin Virol. 2012 Aug;2(4):489-98. doi: 10.1016/j.coviro.2012.05.007. Review.


Survivin is a therapeutic target in Merkel cell carcinoma.

Arora R, Shuda M, Guastafierro A, Feng H, Toptan T, Tolstov Y, Normolle D, Vollmer LL, Vogt A, Dömling A, Brodsky JL, Chang Y, Moore PS.

Sci Transl Med. 2012 May 9;4(133):133ra56. doi: 10.1126/scitranslmed.3003713.


A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing.

Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L, Alexander GJ, Bernal W, Heeney JL.

PLoS One. 2011;6(12):e28879. doi: 10.1371/journal.pone.0028879.

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